Instructions to install and run the Bio-Networking Platform (bionet platform) August 15, 2003 Jun Suzuki (jsuzuki@ics.uci.edu) and Tatsuya Suda (suda@ics.uci.edu) School of Information and Computer Science University of California, Irvine This file contains the instructions to install and start using the bionet platform. The bionet platform is a middleware system that deploy the Bio-Networking Architecture on actual network environments. Please see the following web pages http://netresearch.ics.uci.edu/bionet/ http://netresearch.ics.uci.edu/bionet/resources/platform/ for more details on the Bio-Networking Architecture and bionet platform. I. Requirements - Java runtime environment properly configured and installed (Sun SDK version 1.4 or higher is recommended). - a CORBA implementation (muCORBA or JacORB) installed and properly configured (JacORB is recommended if you are new to the bionet platform). II. Environment Variables You need to configure some environment variables before using the bionet Platform. 5 environment variables; BIONET_HOME, JAVA_HOME, JACORB_HOME, MUCORBA_HOME, and CLIENT_HOME. - BIONET_HOME the root directory of your bionet platform code base - JAVA_HOME the root directory of your Java SDK environment - JACORB_HOME the root directory of your JacORB environment - MUCORBA_HOME the root directory of your muCORBA environment - CLIENT_HOME the root directory of your application (CE) development environment Ex (on your console): set JACORB_HOME=c:\jacorb set BIONET_HOME=c:\apps\bionet set JAVA_HOME=c:\jdk1.4 set CLIENT_HOME=d:\ You can use the command set to check whether you have entered correctly all the necessary envrionment variables. Use the jaco.bat file located in the BIONET_HOME directory to launch the bionet platform. i.e. jaco BioPlatform NOTE: There are two types of bootstrap code in the current distribution of the bionet platform. Bootstrap code is used to start up the bionet platform. One is called BootstrapWithMuCORBA, and the other is called BootstrapWithJacORB. Use Bootstrap when you use muCORBA (a CORBA implementation that bionet research group has been maintaining specific to the bionet platform) as the bionet message transport. BootstrapWithJacORB is to be used with JacORB version 1.4.1 and above, instead of muCORBA. Use Bootstrap if you use JacORB 1.4.0 and below. The files are located in edu.uci.ics.bionet.util. See the documentation about bootstrapping process for more details. III. Directory Structure BIONET_HOME root directory of bionet platform \bin directory tree containing all the binary files of the bionet platform \src directory tree containing all the source code of the bionet platform \doc\javadoc directory tree containing the Javadoc documentations \doc\ppt directory tree containing the PPT documentations jaco.bat batch file used to launch JacORB and on top of that the bionet platfom bionet_properties property file to specify a set of platform configuration properties request_parameter property file to specify the request pattern of the client genetic property file containing the genetic instruction of a CE IV. Inside jaco.bat File The jaco.bat file contains the all the necessary automation to launch the bionet platform. Inside the jaco.bat file is: java -Xbootclasspath/p:%JACORB_HOME%\lib\jacorb.jar -cp %JAVA_HOME%\jre\lib\rt.jar;%JACORB_HOME%\lib\jacorb.jar;%BIONET_HOME%\bin -Dorg.omg.CORBA.ORBClass=org.jacorb.orb.ORB -Dorg.omg.CORBA.ORBSingletonClass=org.jacorb.orb.ORBSingleton -DBIONET_HOME=%BIONET_HOME% %* Launches java with the appropriate boot class path of jacorb, sets the necessary classpaths of JacORB, Java, and Bionet. Loads the necessary system properties from both JacORB and Bionet. So all you have to do is to make sure the 3 environment variables (see Quickstart) are set properly and pointing to the right location and Bionet platform should start running fine. V. Bionet Property File Property files to specify system properties for the Bionet platform. This file is used by the bionet platform and is loaded when the bionet platform loads. The property file currently contains two entries: serializedce.dir= maxthread.num= Ex: serializedce.dir=c:\bionet\serializedce maxthread.num=5 You may modify this file to adjust the configuration of the bionet platform. You can change the location to store the serialized Cyber Entity, or adjust the number of threads allowed in the bionet platform to improve performance. VI. How to get JacORB ready Obtain JacORB from www.jacorb.org. The easiest way to get JacORB to run is to obtain ANT from http://jakarta.apache.org/ant/. Use ANT to rebuild JacORB so that it will be relative to the configuration of your machine. Otherwise you must update the class paths and directory manually. Follow this link to find more about CORBA and JacORB, http://netresearch.ics.uci.edu/bionet/resources/platform/corba/. Here you can find links to tutorials and How Tos documentations. V. Special Thanks We would like to thank the following people who have contributed to the impplementation and maintenance of the bionet platform. Mike Lee (mvle@uci.edu) Khanh Huynh (khanhph@uci.edu) Kevin Nguyen (nguyencp@uci.edu) Jeffrey Ma (jcma@uci.edu) Jasmine Yau (hyau@uci.edu) Ling Qi (lqi@uci.edu) Tammy Hwang (youngwonee@hotmail.com) Sonya Gupta (stgupta@uci.edu) Victor Ni (niz@uci.edu)